We present the lexico-semantic foundations underlying a multilingual lexicon the entries of which are constituted by so-called subwords. These subwords reflect semantic atomicity constraints in the medical domain which diverge from canonical lexicological understanding in NLP. We focus here on criteria to identify and delimit reasonable subword units, to group them into functionally adequate synonymy classes and relate them by two types of lexical relations. The lexicon we implemented on the basis of these considerations forms the lexical backbone for MorphoSaurus, a cross-language document retrieval engine for the medical domain.